You can make the mute button come back when filtering by including the is:unread filter and adding -is:muted. I have the following query displayed beneath my inbox using the Multiple Inboxes lab, and it allows me to mute conversations:
label:Support is:unread -is:muted
This shows me anything labelled Support that I haven't read, and that isn't muted yet. ...

It is a bug in the system.
You will need to collect your messages without the label:yourlabel search.
i.e. When you are creating/editing the filter, do a Test Search based on your filter. This will bring up all the results.
From here you will find the once missing Mute Option in the More Actions Menu for each message.
A second way would be have a second ...

I believe Google has disabled the keyboard shortcut for muting a video call using the spacebar, so I don't believe this is going to be too much of a problem now.
I can suggest, however, is to lock the keyboard if you are on the video call, which prevents toddlers from accidentally pressing on any keyboard buttons while on the video call, but you can try ...